Nextflow workflow report

[gigantic_goldberg]

Workflow execution completed unsuccessfully!

The exit status of the task that caused the workflow execution to fail was: 255.

The full error message was:

Error executing process > 'callVariants (4)'

Caused by:
  Process `callVariants (4)` terminated with an error exit status (255)

Command executed:

  echo "Starting BCFTools from within the container for MAX_M07792_2.00 on dataset JD32HPP..."
  
  bcftools mpileup -Ou -f "input-dir-cluster/refs/GRCh38_no_alt_GCA_000001405.15.fasta.gz" -T "MAX_M07792_2.00_TOBIAS_TF_binding_sites-sorted.bed" -b "JD32HPP.bamlist.txt" --annotate FORMAT/AD,FORMAT/DP | bcftools call -Ou -mv | bcftools filter -i'QUAL>10' | bcftools +fill-tags - -- -t AF,VAF > "MAX_M07792_2.00_qualgt10.var.flt.VAF.allTFBS_JD32HPP.vcf"

Command exit status:
  255

Command output:
  Starting BCFTools from within the container for MAX_M07792_2.00 on dataset JD32HPP...

Command error:
  Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid
  [E::fai_build3_core] Failed to open the file input-dir-cluster/refs/GRCh38_no_alt_GCA_000001405.15.fasta.gz : No such file or directory
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type
  Failed to read from standard input: unknown file type

Work dir:
  /scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work/08/1ae3ec81099a4e64eab7955eacddac

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`
Run times
27-Feb-2024 19:36:06 - 27-Feb-2024 20:10:26 (duration: 34m 20s)
  1366 succeeded  
  0 cached  
  0 ignored  
  1 failed  
Nextflow command
nextflow run -resume main.nf --run_mode subset --dataset_id_list input-dir-cluster/manifests/dataset-manifest-heme-cancers.txt --genome_fasta input-dir-cluster/refs/GRCh38_no_alt_GCA_000001405.15.fasta.gz --output_dir output-dir-cluster -c nextflow_cluster.config -with-dag workflow-reports/dag-20240227-19.35.html -with-report workflow-reports/report-20240227-19.35.html -with-timeline workflow-reports/timeline-20240227-19.35.html
CPU-Hours
1.1 (0.1% failed)
Launch directory
/scratch/users/ntu/suffiazi/tfbs-variant-calling-nf
Work directory
/scratch/users/ntu/suffiazi/tfbs-variant-calling-nf/work
Project directory
/scratch/users/ntu/suffiazi/tfbs-variant-calling-nf
Script name
main.nf
Script ID
4af21cf2ab88a8442835b8986f4f9a49
Workflow session
140920df-0168-40f6-86d5-6f6c04264f45
Workflow profile
standard
Workflow container
/home/users/ntu/suffiazi/apps/sifs/bcftools-py.sif
Container engine
singularity
Nextflow version
version 23.10.1, build 5891 (12-01-2024 22:01 UTC)

Resource Usage

These plots give an overview of the distribution of resource usage for each process.

CPU

Memory

Job Duration

I/O

Tasks

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(tasks table omitted because the dataset is too big)